﻿<?xml version="1.0" encoding="utf-8" ?>
<AutomationTest>
  <SmallSAMFile>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.sam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <RecordTagKeys>VN,SN,LN,ID,PU,LB,SM,ID,PU,LB,SM</RecordTagKeys>
    <RecordTagValues>1.0,chr20,62435964,L1,SC_1_10,SC_1,NA12891,L2,SC_2_12,SC_2,NA12891</RecordTagValues>
    <HeaderTyeps>HD,SQ,RG,RG</HeaderTyeps>
  </SmallSAMFile>
  <SAMFileWithAllFields>
    <FilePath>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.sam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.sam</FilePath1>
    <ExpectedSequence>TestUtils\SAMBAMTestData\qualitativesequences.fa</ExpectedSequence>
    <ScoresCount>35</ScoresCount>
    <ExpectedAlignedSeqCount>11</ExpectedAlignedSeqCount>
    <ExpectedSeqWithPointers>GCAATGATAAAAGGAGTAACCTGTGAAAAAGATGC</ExpectedSeqWithPointers>
    <LineNumberToPoint>3</LineNumberToPoint>
    <VirtualAlignedSeqCount>11</VirtualAlignedSeqCount>
    <CIGAR>35M</CIGAR>
  </SAMFileWithAllFields>
  <SAMFileWithRef>
    <FilePath>TestUtils\SAMBAMTestData\AlignmentWithRef.sam</FilePath>
    <ReferenceSeq>TestUtils\SAMBAMTestData\ref_list.fna</ReferenceSeq>
    <ExpectedSequence>TestUtils\SAMBAMTestData\RefSequencesOutput.fa</ExpectedSequence>
  </SAMFileWithRef>
  <SmallSizeBAMFile>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <RecordTagKeys>VN,SN,LN,ID,PU,LB,SM,ID,PU,LB,SM</RecordTagKeys>
    <RecordTagValues>1.0,chr20,62435964,L1,SC_1_10,SC_1,NA12891,L2,SC_2_12,SC_2,NA12891</RecordTagValues>
    <HeaderTyeps>HD,SQ,RG,RG</HeaderTyeps>
    <ChromosomeName>chr20</ChromosomeName>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <AlignedSeqCount>2</AlignedSeqCount>
  </SmallSizeBAMFile>
  <SeqRangeBAMFile>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutputWithIndex.fa</ExpectedSequence>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <RecordTagKeys>VN,SN,LN,ID,PU,LB,SM,ID,PU,LB,SM</RecordTagKeys>
    <RecordTagValues>1.0,chr20,62435964,L1,SC_1_10,SC_1,NA12891,L2,SC_2_12,SC_2,NA12891</RecordTagValues>
    <HeaderTyeps>HD,SQ,RG,RG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <AlignedSeqCount>1</AlignedSeqCount>
    <ChromosomeName>chr20</ChromosomeName>
  </SeqRangeBAMFile>
  <BAMFileWithRefSeq>
    <FilePath>TestUtils\SAMBAMTestData\NA07000.454.BCM.crossmatch.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\NA07000.454.BCM.crossmatchSeqAlignmentOutput.fa</ExpectedSequence>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,bowtie-Se_colireads/e_coli_10000snp.fqec_snp.sam</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>202</EndIndex>
    <AlignedSeqCount>968</AlignedSeqCount>
    <ExpectedSeqWithPointers>GCAATGATAAAAGGAGTAACCTGTGAAAAAGATGC</ExpectedSeqWithPointers>
    <LineNumberToPoint>0</LineNumberToPoint>
    <ChromosomeName>chr20</ChromosomeName>
  </BAMFileWithRefSeq>
  <BAMTOSAMConversion>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\SeqAlignment.sam</FilePath1>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutputWithIndex.fa</ExpectedSequence>
    <RecordTagKeys>VN,SN,LN,ID,PU,LB,SM,ID,PU,LB,SM</RecordTagKeys>
    <RecordTagValues>1.0,chr20,62435964,L1,SC_1_10,SC_1,NA12891,L2,SC_2_12,SC_2,NA12891</RecordTagValues>
    <ExpectedSeqWithPointers>AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG</ExpectedSeqWithPointers>
    <LineNumberToPoint>0</LineNumberToPoint>
    <HeaderTyeps>HD,SQ,RG,RG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>178</EndIndex>
    <AlignedSeqCount>1</AlignedSeqCount>
  </BAMTOSAMConversion>
  <BAMFileWithMultipleAlignedSeqs>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignmentWithRef.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\SeqAlignmentWithRef.bam</FilePath1>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentWithRefSeq.fa</ExpectedSequence>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,\bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam\</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <AlignedSeqCount>968</AlignedSeqCount>
    <ChromosomeName>chr20</ChromosomeName>
  </BAMFileWithMultipleAlignedSeqs>
  <BAMFileFormatWithMultipleAlignedSeqs>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignmentWithRef.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\SeqAlignmentWithRef.bam</FilePath1>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentFormatWithRef.fa</ExpectedSequence>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,\bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam\</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <AlignedSeqCount>968</AlignedSeqCount>
    <ChromosomeName>chr20</ChromosomeName>
  </BAMFileFormatWithMultipleAlignedSeqs>
  <BAMFileWithQualityValues>
    <FilePath>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.fa</ExpectedSequence>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,\"bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam\</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <Cigars>35M,35M,35M,35M,35M,35M,35M,35M,35M,35M,35M</Cigars>
    <Bins>4681,4681,4681,4681,4681,4681,4681,4681,4681,4681,4681</Bins>
    <QNames>r0,r1,r2,r3,r4,r5,r6,r7,r8,r9,r10</QNames>
    <AlignedSeqCount>11</AlignedSeqCount>
    <ChromosomeName>chr20</ChromosomeName>
  </BAMFileWithQualityValues>
  <BAMFileWithSequenceRangeSeqs>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\AlignmentWithSequenceRange.fa</ExpectedSequence>
    <RecordTagKeys>VN,SN,LN,ID,PU,LB,SM,ID,PU,LB,SM</RecordTagKeys>
    <RecordTagValues>1.0,chr20,62435964,L1,SC_1_10,SC_1,NA12891,L2,SC_2_12,SC_2,NA12891</RecordTagValues>
    <HeaderTyeps>HD,SQ,RG,RG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <AlignedSeqCount>1</AlignedSeqCount>
    <ChromosomeName>chr20</ChromosomeName>
  </BAMFileWithSequenceRangeSeqs>
  <BAMFileWithSequenceRangeRefSeqs>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\AlignmentWithSequenceRefName.fa</ExpectedSequence>
    <RecordTagKeys>VN,SN,LN,ID,PU,LB,SM,ID,PU,LB,SM</RecordTagKeys>
    <RecordTagValues>1.0,chr20,62435964,L1,SC_1_10,SC_1,NA12891,L2,SC_2_12,SC_2,NA12891</RecordTagValues>
    <HeaderTyeps>HD,SQ,RG,RG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>28833</EndIndex>
    <AlignedSeqCount>2</AlignedSeqCount>
    <ChromosomeName>chr20</ChromosomeName>
  </BAMFileWithSequenceRangeRefSeqs>
  <MediumSizeBAMFile>
    <FilePath>TestUtils\SAMBAMTestData\MediumSizeBam.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\MediumSizeBAMSequences.fa</ExpectedSequence>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,\"bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam\</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>5783</EndIndex>
    <AlignedSeqCount>586</AlignedSeqCount>
    <ChromosomeName>gi|110640213|ref|NC_008253.1|</ChromosomeName>
    <MediumSizeBAMSortOutputMatchReadNames>TestUtils\SAMBAMTestData\MediumSizeBAMSortOutputMatchReadNames.txt</MediumSizeBAMSortOutputMatchReadNames>
    <MediumSizeBAMSortOutputMatchChromosomeCoordinates>TestUtils\SAMBAMTestData\MediumSizeBAMSortOutputMatchChromosomeCoordinates.txt</MediumSizeBAMSortOutputMatchChromosomeCoordinates>
    <MediumSizeBAMSortOutputMatchChromosomeNameAndCoordinates>TestUtils\SAMBAMTestData\MediumSizeBAMSortOutputMatchChromosomeNameAndCoordinates.txt</MediumSizeBAMSortOutputMatchChromosomeNameAndCoordinates>
  </MediumSizeBAMFile>
  <MediumSizeBAMFileWithSmallerEndIndex>
    <FilePath>TestUtils\SAMBAMTestData\MediumSizeBam.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\AlignmentWithIndexTwelveOutput.fa</ExpectedSequence>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,\"bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam\</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>98</EndIndex>
    <AlignedSeqCount>12</AlignedSeqCount>
    <ChromosomeName>gi|110640213|ref|NC_008253.1|</ChromosomeName>
  </MediumSizeBAMFileWithSmallerEndIndex>
  <MediumSizeBAMFileWithRefIndex>
    <FilePath>TestUtils\SAMBAMTestData\MediumSizeBam.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentWithRefSeq.fa</ExpectedSequence>
    <RecordTagKeys>VN,SO,SN,LN,ID,VN,CL</RecordTagKeys>
    <RecordTagValues>1.0,unsorted,gi|110640213|ref|NC_008253.1|,4938920,Bowtie,0.11.3,\"bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam\</RecordTagValues>
    <HeaderTyeps>HD,SQ,PG</HeaderTyeps>
    <RefIndex>0</RefIndex>
    <StartIndex>0</StartIndex>
    <EndIndex>5783</EndIndex>
    <AlignedSeqCount>968</AlignedSeqCount>
    <ChromosomeName>gi|110640213|ref|NC_008253.1|</ChromosomeName>
  </MediumSizeBAMFileWithRefIndex>
  <BAMAlignedSeqProperties>
    <FilePath>TestUtils\SAMBAMTestData\MediumSizeBam.bam</FilePath>
    <BAMIndexFile>TestUtils\SAMBAMTestData\SeqAlignment.bam.bai</BAMIndexFile>
    <FlagValue>QueryOnReverseStrand</FlagValue>
    <ISize>0</ISize>
    <MapQ>255</MapQ>
    <Metadata>1</Metadata>
    <MPos>0</MPos>
    <OptionalFields>3</OptionalFields>
    <Pos>5212</Pos>
    <QueryLength>35</QueryLength>
    <RName>gi|110640213|ref|NC_008253.1|</RName>
  </BAMAlignedSeqProperties>
  <SAMToBAMConversionForMultipleAlignedSeq>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignmentWithRef.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\AlignmentWithRef.sam</FilePath1>
  </SAMToBAMConversionForMultipleAlignedSeq>
  <SAMToBAMConversionForMultipleAlignedSeqWithDV>
    <FilePath>TestUtils\SAMBAMTestData\AlignmentQualitySequenceWithDV.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\AlignmentWithRef.sam</FilePath1>
  </SAMToBAMConversionForMultipleAlignedSeqWithDV>
  <BAMToSAMConversionForQualitySeqs>
    <FilePath>TestUtils\SAMBAMTestData\BAMWithQualityValues.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.sam</FilePath1>
  </BAMToSAMConversionForQualitySeqs>
  <SAMToBAMConversionForQualitySeqs>
    <FilePath>TestUtils\SAMBAMTestData\BAMWithQualityValues.bam</FilePath>
    <FilePath1>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.sam</FilePath1>
  </SAMToBAMConversionForQualitySeqs>
  <BAMIndex>
    <FilePath>TestUtils\SAMBAMTestData\AlignmentWithQualityValues.bam</FilePath>
    <BAMIndexCount>1</BAMIndexCount>
  </BAMIndex>
  <InvalidBAMFile>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.sam</FilePath>
  </InvalidBAMFile>
  <EmptySamFile>
    <FilePath>TestUtils\SAMBAMTestData\EmptySAMFile.fa</FilePath>
  </EmptySamFile>
  <OneEmptySequenceSamFile>
    <FilePath>TestUtils\SAMBAMTestData\EmptyReaderLine.sam</FilePath>
    <ExpectedSequence>GCAATGATAAAAGGAGTAACCTGTGAAAAAGATGC</ExpectedSequence>
  </OneEmptySequenceSamFile>
  <InvalidSamMBFReader>
    <FilePath>TestUtils\SAMBAMTestData\InvalidSamBioReader.sam</FilePath>
  </InvalidSamMBFReader>
  <InvalidEmptyLine>
    <FilePath>TestUtils\SAMBAMTestData\InvalidSAMEmptyFile.sam</FilePath>
  </InvalidEmptyLine>
  <SamFormatterFile>
    <FilePath>TestUtils\SAMBAMTestData\SamFormatterFile.sam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqFormatterAlignOutput.fa</ExpectedSequence>
  </SamFormatterFile>
  <MediumSizeFile>
    <FilePath>TestUtils\SAMBAMTestData\MediumSizeSAMFile.sam</FilePath>
    <ReferenceSeq>TestUtils\SAMBAMTestData\ref_list.fna</ReferenceSeq>
    <ExpectedSequence>TestUtils\SAMBAMTestData\RefSequencesOutput.fa</ExpectedSequence>
    <ExpectedAlignedSeqCount>2390</ExpectedAlignedSeqCount>
    <FirstBlockSequence>TAACCCTAACCCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCTAACCT</FirstBlockSequence>
    <MiddleBlockSequence>GCTCCTCGGAGCAGGAAGTCCATGGGGTCTCTGCTGAGACTGGAGCATGCTCTTCCCACCCTCATTCTGCTCTTGGTGTCCTTTTGCAGAGCCCCGGG</MiddleBlockSequence>
    <LastBlockSequence>CTTGTCTTAAGATGTACCCTATTACTCAGAAGGGCTTATTGGGATACTGACATGTGTATTTTCTTGATTTGACTCTGCAGTTCCTCATCAGAAGGAAGTACTTCATCAATTACGTCCTCTTCATATTCATCAATTTCTTCCCCATCATACTCATCTTCGCTTCCCACATCACTTCCTGACACCTCTGCCTCATCCTCCAGGTATTTCCTCAACCTCCTA</LastBlockSequence>
  </MediumSizeFile>
  <PairedReadForSmallFile>
    <FilePath>TestUtils\SAMBAMTestData\SeqAlignment.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <PairedReadsCount>2</PairedReadsCount>
    <Mean>200</Mean>
    <deviation>50</deviation>
    <InsertLength>0,0</InsertLength>
    <PairedReadType>Orphan,Orphan</PairedReadType>
    <LibraryName>2K</LibraryName>
  </PairedReadForSmallFile>
  <PairedReadTypes>
    <FilePath>TestUtils\SAMBAMTestData\BAMFileWithPairedReads.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <PairedReadsCount>2</PairedReadsCount>
    <Mean>200</Mean>
    <deviation>50</deviation>
    <InsertLength>0,0</InsertLength>
    <PairedReadType>Chimera,MultipleHits,Orphan,Chimera,Orphan,LengthAnomaly</PairedReadType>
    <LibraryName>2K</LibraryName>
  </PairedReadTypes>
  <PairedReadTypesForMeanAndDeviation>
    <FilePath>TestUtils\SAMBAMTestData\BAMFileWithPairedReads.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <PairedReadsCount>2</PairedReadsCount>
    <Mean>200</Mean>
    <deviation>50</deviation>
    <InsertLength>0,0</InsertLength>
    <PairedReadType>Chimera,MultipleHits,Orphan,Chimera,Orphan,Normal</PairedReadType>    
    <LibraryName>2K</LibraryName>
  </PairedReadTypesForMeanAndDeviation>
  <PairedReadTypesForReads>
    <FilePath>TestUtils\SAMBAMTestData\BAMFileWithPairedReads.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <PairedReadsCount>2</PairedReadsCount>
    <Mean>200</Mean>
    <deviation>50</deviation>
    <InsertLength>0,0</InsertLength>
    <PairedReadType>Chimera,Chimera,Chimera,LengthAnomaly</PairedReadType>
    <LibraryName>2K</LibraryName>
  </PairedReadTypesForReads>
  <PairedReadTypesForLibraryInfo>
    <FilePath>TestUtils\SAMBAMTestData\BAMFileWithPairedReads.bam</FilePath>
    <ExpectedSequence>TestUtils\SAMBAMTestData\SeqAlignmentOutput.fa</ExpectedSequence>
    <PairedReadsCount>2</PairedReadsCount>
    <Mean>200</Mean>
    <deviation>50</deviation>
    <InsertLength>0,0,0,0,0,214</InsertLength>
    <PairedReadType>Chimera,Chimera,Orphan,Chimera,Orphan,LengthAnomaly</PairedReadType>
    <LibraryName>2K</LibraryName>
  </PairedReadTypesForLibraryInfo>
</AutomationTest>